 |
 |
 |
 |
 |
 |
Sains Malaysiana 47(8)(2018): 1709–1723 http://dx.doi.org/10.17576/jsm-2018-4708-10
Cloning
and Analysis of the Eg4CL1 Gene and Its Promoter from Oil Palm (Elaeis
guineensis Jacq.)
(Pengklonan
dan Analisis Gen Eg4CL1 dan Promoternya daripada Kelapa Sawit (Elaeis
guineensis Jacq.))
YUSUF CHONG
YU
LOK1,2,
IDRIS
ABU
SEMAN3,
NOR
AINI
AB
SHUKOR4,5,
MOHD
NORFAIZULL
MOHD
NOR6
& MOHD PUAD ABDULLAH6*
1Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA,
Kampus Jasin, 77300 Merlimau, Melaka, Malaysia
2Agricultural Biotechnology Research Group, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
3Malaysian Palm Oil Board (MPOB), No 6, Persiaran Institusi,
Bandar Baru Bangi, 43000 Kajang, Selangor Darul Ehsan, Malaysia
4Department of Forest Management, Faculty of Forestry, Universiti
Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
5Institute
of Tropical Forestry and Forest Product, Universiti Putra Malaysia,
43400 UPM
Serdang, Selangor Darul Ehsan, Malaysia
6Department
of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular
Sciences, Universiti
Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
Received: 9 September 2016/Accepted: 26 April 2018
ABSTRACT
The empty fruit bunches of oil palm have been used as the raw material
to produce biofuel. However, the lignin present in oil palm tissues
hampers the enzymatic saccharification of lignocellulosic biomass
and lower the yield of biofuel produced. Hence, various efforts
were taken to identify the lignin biosynthetic genes in oil palm
and to investigate their regulation at the molecular level. In this
study, a lignin biosynthetic gene, Eg4CL1 and its promoter were isolated from the
oil palm. Eg4CL1 contains the acyl-activating enzyme
consensus motif and boxes I & II which are present in other
4CL homologs. Eg4CL1 was clustered together with
known type I 4CL proteins involved in lignin biosynthesis
in other plants. Gene expression analysis showed that Eg4CL1
was expressed abundantly in different organs of oil palm throughout
the course of development, reflecting its involvement in lignin
biosynthesis in different organs at all stages of growth. The presence
of the lignification toolbox - AC elements in the 1.5 kb promoter
of Eg4CL1 further suggests the potential role of the gene
in lignin biosynthesis in oil palm. Together, these results suggested
that Eg4CL1 is a potential candidate gene involved in lignin
biosynthesis in oil palm.
Keywords: Biofuel; lignin; oil palm; promoter; 4CL
ABSTRAK
Tandan kosong buah kelapa sawit telah digunakan sebagai bahan asas
untuk menghasilkan biofuel. Walau bagaimanapun, lignin yang terdapat
dalam tisu kelapa sawit menghalang proses sakarifikasi enzimatik
biojisim lignoselulosa dan mengurangkan hasil bahan api biologi
yang dihasilkan. Oleh itu, pelbagai usaha telah diambil untuk mengenal
pasti gen biosintesis lignin dalam kelapa sawit dan untuk mengkaji
pengawalaturannya pada peringkat molekul. Dalam kajian ini, gen
biosintesis lignin, Eg4CL1 dan promoternya
telah dipencilkan daripada kelapa sawit. Eg4CL1 mengandungi
motif konsensus enzim pengaktifan asil dan kotak I & II yang
terdapat dalam homolog 4CL yang lain. Eg4CL1 berkelompok
bersama dengan protein 4CL yang diketahui terlibat
dalam biosintesis lignin dalam tumbuhan lain. Analisis pengekspresan
gen menunjukkan bahawa Eg4CL1 diekspres dengan banyak dalam
organ kelapa sawit yang berbeza pada semua peringkat pertumbuhan,
mencerminkan penglibatannya dalam biosintesis lignin dalam organ
yang berbeza pada semua peringkat pertumbuhan. Kehadiran peti alat
lignifikasi - unsur AC dalam promoter Eg4CL1 1.5 kb selanjutnya
menyokong potensi gen ini yang berperanan dalam biosintesis lignin
pada pokok kelapa sawit. Secara keseluruhannya, keputusan kajian
ini mencadangkan Eg4CL1 sebagai calon gen yang berpotensi
terlibat dalam biosintesis lignin pada pokok kelapa sawit.
Kata kunci: Biofuel; kelapa sawit; lignin;
promoter; 4CL
REFERENCES
Bahariah, B., Parveez, G.K.A., Masani, M.Y.A., Masura, S.S.,
Khalid, N. & Othman, R.Y. 2013. Biolistic transformation of oil palm using
the phosphomannose isomerase (pmi) gene as a positive selectable marker. Biocatalysis
and Agricultural Biotechnology 2: 295-304.
Baumann, K., De Paolis, A., Costantino, P. & Gualberti,
G. 1999. The DNA binding site of the dof protein NtBBF1 is essential for
tissue-specific and auxin-regulated expression of the rolb oncogene in plants. The
Plant Cell 11: 323-334.
Carroll, B.J., Klimyuk, V.I., Thomas, C.M., Bishop, G.J.,
Harrison, K., Scofield, S.R. & Jones, J.D. 1995. Germinal transpositions of
the maize element dissociation from T-DNA loci in tomato. Genetics 139:
407-420.
Chao, N., Liu, S.X., Liu, B.M., Li, N., Jiang, X.N. &
Gai, Y. 2014. Molecular cloning and functional analysis of nine cinnamyl
alcohol dehydrogenase family members in Populus tomentosa. Planta 240:
1097-1112.
Chapple, C., Ladisch, M. & Meilan, R. 2007. Loosening lignin's
grip on biofuel production. Nature Biotechnology 25: 746-
748. Chen, F. & Dixon, R.A. 2007. Lignin modification
improves fermentable sugar yields for biofuel production. Nature
Biotechnology 25: 759-761.
Ehlting, J., Büttner, D., Wang, Q., Douglas, C.J., Somssich,
I.E. & Kombrink, E. 1999. Three 4-Coumarate: Coenzyme A ligases in Arabidopsis
thaliana represent two evolutionarily divergent classes in angiosperms. Plant
Journal 19: 9-20.
Filichkin, S.A., Leonard, J.M., Monteros, A., Liu, P.P.
& Nonogaki, H. 2004. A novel endo-beta-mannanase gene in tomato LeMAN5 is
associated with anther and pollen development. Plant Physiology 134:
1080-1087.
Fu, C., Xiao, X., Xi, Y., Ge, Y., Chen, F., Bouton, J.,
Dixon, R.A. & Wang, Z.Y. 2011. Downregulation of cinnamyl alcohol
dehydrogenase (CAD) leads to improved saccharification efficiency in
switchgrass. Bioenergy Research 4: 153-164.
Gao, D., Haarmeyer, C., Balan, V., Whitehead, T.A., Dale,
B.E. & Chundawat, S.P. 2014. Lignin triggers irreversible cellulase loss
during pretreated lignocellulosic biomass saccharification. Biotechnology
for Biofuels 7: 175.
Gao, S., Yu, H.N., Xu, R.X., Cheng, A.X. & Lou, H.X.
2015. Cloning and functional characterization of a 4-coumarate COA ligase from
liverwort Plagiochasma appendiculatum. Phytochemistry 111: 48-58.
Goda, H., Sawa, S., Asami, T., Fujioka, S., Shimada, Y.
& Yoshida, S. 2004. Comprehensive comparison of auxin-regulated and
brassinosteroid-regulated genes in Arabidopsis. Plant Physiology 134:
1555-1573.
Goebels, C., Thonn, A., Gonzalez-Hilarion, S., Rolland, O.,
Moyrand, F., Beilharz, T.H. & Janbon, G. 2013. Introns regulate gene
expression in Cryptococcus neoformans in a Pab2p dependent pathway. PLoS
Genetics 9(8): e1003686.
Grierson, C., Du, J.S., Zabala, M., Beggs, K., Smith, C.,
Holdsworth, M. & Bevan, M. 1994. Separate cis sequences and trans factors direct metabolic and developmental regulation of a potato tuber
storage protein gene. Plant Journal 5: 815-826.
Gui, J., Shen, J. & Li, L. 2011. Functional
characterization of evolutionarily divergent 4-coumarate: Coenzyme A ligases in
rice. Plant Physiology 157: 574-586.
Hall, T.A. 1999. BioEdit: A user-friendly biological
sequence alignment editor and analysis program for windows 95/98/ NT. Nucleic
Acids Symposium Series 41: 95-98.
Hamberger, B., Ellis, M., Friedmann, M., de Azevedo Souza,
C., Barbazuk, B. & Douglas, C.J. 2007. Genome-wide analyses of
phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: The populus lignin toolbox and conservation and
diversification of angiosperm gene families. Canadian Journal of Botany 85:
1182-1201.
Hamberger, B. & Hahlbrock, K. 2004. The 4-coumarate: CoA
ligase gene family in Arabidopsis thaliana comprises one rare,
sinapate-activating and three commonly occurring isoenzymes. Proceedings of
the National Academy of Sciences of the United States of America 101:
2209-2214.
Hatton, D., Sablowski, R., Yung, M.H., Smith, C., Schuch, W. & Bevan, M. 1995. Two classes of cis sequences contribute to tissue-specific expression of a pal2 promoter in transgenic tobacco. The Plant Journal 7: 859-876. Heath, R., McInnes, R., Lidgett,
A., Huxley, H., Lynch, D., Jones, E., Mahoney, N. & Spangenberg,
G. 2002. Isolation and characterisation of three 4-coumarate: Coa-ligase
homologue cdnas from Perennial Ryegrass (Lolium perenne).
Journal of Plant Physiology 159: 773-779. Hirano, K., Kondo, M., Aya, K., Miyao, A., Sato,
Y., Antonio, B.A., Namiki, N., Nagamura, Y. & Matsuoka, M. 2013.
Identification of transcription factors involved in rice secondary cell wall
formation. Plant and Cell Physiology 54: 1791-1802.
Hu, W.J., Kawaoka, A., Tsai, C.J., Lung, J.,
Osakabe, K., Ebinuma, H. & Chiang, V.L. 1998. Compartmentalized expression
of two structurally and functionally distinct 4-coumarate: CoA ligase genes in
Aspen (Populus tremuloides). Proceedings of the National Academy of
Sciences of the United States of America 95: 5407-5412.
Hu, Y., Gai, Y., Yin, L., Wang, X., Feng, C.,
Feng, L., Li, D., Jiang, X.N. & Wang, D.C. 2010. Crystal structures of a populus
tomentosa 4-coumarate: CoA ligase shed light on its enzymatic mechanisms. The
Plant Cell 22: 3093-3104.
Huang, J., Gu, M., Lai, Z., Fan, B., Shi, K.,
Zhou, Y.H., Yu, J.Q. & Chen, Z. 2010. Functional analysis of the Arabidopsis
PAL gene family in plant growth, development, and response to environmental
stress. Plant Physiology 153: 1526-1538.
Ibrahim, M.F., Abd-Aziz, S., Yusoff, M.E.M.,
Phang, L.Y. & Hassan, M.A. 2015. Simultaneous enzymatic saccharification
and ABE fermentation using pretreated oil palm empty fruit bunch as substrate
to produce butanol and hydrogen as biofuel. Renewable Energy 77:
447-455.
Jung, J.H., Vermerris, W., Gallo, M., Fedenko,
J.R., Erickson, J.E. & Altpeter, F. 2013. RNA interference suppression of
lignin biosynthesis increases fermentable sugar yields for biofuel production
from field-grown sugarcane. Plant Biotechnology Journal 11: 709-716.
Kumar, A. & Ellis, B.E. 2003. 4-Coumarate:
CoA ligase gene family in Rubus idaeus: cDNA structures, evolution, and
expression. Plant Molecular Biology 51: 327-340.
Kizis, D. & Pagès, M. 2002. Maize
DRE-binding proteins DBF1 and DBF2 are involved in rab17 regulation through the
drought-responsive element in an ABA-dependent pathway. The Plant Journal 30:
679-689.
Kropat, J., Tottey, S., Birkenbihl, R.P., Depege,
N., Huijser, P. & Merchant, S. 2005. A regulator of nutritional
copper signaling in chlamydomonas is an SBP domain protein that
recognizes the GTAC core of copper response element. Proceedings
of the National Academy of Sciences of the United States of America
102: 18730-18735. Lee, D., Ellard, M., Wanner, L.A., Davis, K.R.
& Douglas, C.J. 1995. The Arabidopsis thaliana 4-coumarate: CoA
ligase (4CL) gene: Stress and developmentally regulated expression and
nucleotide sequence of its cDNA. Plant Molecular Biology 28: 871-884.
Lescot, M., Déhais, P., Thijs, G., Marchal, K.,
Moreau, Y., Van de Peer, Y., Rouzé, P. & Rombauts, S. 2002. PlantCARE, a
database of plant cis-acting regulatory elements and a portal to tools
for in silico analysis of promoter sequences. Nucleic Acids Research 30:
325-327.
Li, Y., Im Kim, J., Pysh, L. & Chapple, C.
2015. Four isoforms of Arabidopsis thaliana 4-coumarate: CoA ligase
(4CL) have overlapping yet distinct roles in phenylpropanoid metabolism. Plant
Physiology 169: 2409-2421.
Li, Z.B., Li, C.F., Li, J. & Zhang, Y.S. 2014.
Molecular cloning and functional characterization of two divergent
4-coumarate: coenzyme A ligases from Kudzu (Pueraria lobata).
Biological & Pharmaceutical Bulletin 37: 113-122. Marchler-Bauer, A., Lu, S., Anderson, J.B.,
Chitsaz, F., Derbyshire, M.K., DeWeese-Scott, C., Fong, J.H., Geer, L.Y., Geer,
R.C., Gonzales, N.R. & Gwadz, M. 2010. CDD: A conserved domain database for
the functional annotation of proteins. Nucleic Acids Research 39:
225-229.
Masani, M.Y.A., Noll, G.A., Parveez, G.K.A.,
Sambanthamurthi, R. & Prüfer, D. 2014. Efficient transformation of oil palm
protoplasts by peg-mediated transfection and DNA microinjection. PloS One doi.
10.1371/journal.pone.0096831.
Mena, M., Cejudo, F.J., Isabel-Lamoneda, I.
& Carbonero, P. 2002. A role for the DOF transcription factor BPBF in the
regulation of gibberellin-responsive genes in Barley Aleurone. Plant
Physiology 130: 111-119.
Nagaya, S., Kawamura, K., Shinmyo, A. &
Kato, K. 2009. The HSP terminator of Arabidopsis thaliana increases gene
expression in plant cells. Plant and Cell Physiology 51: 328-332.
Neutelings, G. 2011. Lignin variability in plant
cell walls: Contribution of new models. Plant Science 181: 379-386.
Nordin, K., Vahala, T. & Palva, E.T. 1993.
Differential expression of two related, low-temperature-induced genes in Arabidopsis
thaliana (L.) Heynh. Plant Molecular Biology 21: 641-653.
Ochman, H., Gerber, A.S. & Hartl, D.L. 1988.
Genetic applications of an inverse polymerase chain reaction. Genetics 120:
621-623.
Park, H.C., Kim, M.L., Kang, Y.H., Jeon, J.M.,
Yoo, J.H., Kim, M.C., Park, C.Y., Jeong, J.C., Moon, B.C., Lee, J.H. &
Yoon, H.W. 2004. Pathogen- and NaCl-induced expression of the SCaM-4 promoter
is mediated in part by a GT-1 box that interacts with a GT-1-like transcription
factor. Plant Physiology 135: 2150-2161.
Piarpuzan, D., Quintero, J.A. & Cardona,
C.A. 2011. Empty fruit bunches from oil palm as a potential raw material for
fuel ethanol production. Biomass and Bioenergy 35: 1130-1137.
Raes, J., Rohde, A., Christensen, J.H., Van de
Peer, Y. & Boerjan, W. 2003. Genome-wide characterization of the
lignification toolbox in Arabidopsis. Plant Physiology 133: 1051-1071.
Rao, G., Pan, X., Xu, F., Zhang, Y., Cao, S.,
Jiang, X. & Lu, H. 2015. Divergent and overlapping function of five
4-Coumarate/Coenzyme A ligases from Populus tomentosa. Plant
Molecular Biology Reporter 33: 841-854.
Rastogi, S., Kumar, R., Chanotiya, C.S.,
Shanker, K., Gupta, M.M., Nagegowda, D.A. & Shasany, A.K. 2013.
4-Coumarate: CoA ligase partitions metabolites for eugenol biosynthesis. Plant
and Cell Physiology 54: 1238-1252.
Rose, A., Meier, I. & Wienand, U. 1999. The tomato i-box binding factor LeMYBI is a member of a novel class of myb-like proteins. The Plant Journal 20: 641-652. Rubio-Somoza, I., Martinez, M., Abraham, Z., Diaz,
I. & Carbonero, P. 2006. Ternary complex formation between HvMYBS3
and other factors involved in transcriptional control in barley
seeds. Plant Journal 47: 269-281. Shen, H., Mazarei, M., Hisano, H.,
Escamilla-Trevino, L., Fu, C., Pu, Y., Rudis, M.R., Tang, Y., Xiao, X.,
Jackson, L. & Li, G. 2013. A genomics approach to deciphering lignin
biosynthesis in switchgrass. The Plant Cell 25: 4342-4361.
Shen, H., He, X., Poovaiah, C.R., Wuddineh,
W.A., Ma, J., Mann, D.G., Wang, H., Jackson, L., Tang, Y., Neal Stewart, C.
& Chen, F. 2012. Functional characterization of the switchgrass (Panicum
virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of
lignocellulosic feedstocks. New Phytologist 193: 121-136.
Silber, M.V., Meimberg, H. & Ebel, J. 2008.
Identification of a 4-Coumarate: CoA ligase gene family in the moss,
Physcomitrella patens Q. Phytochemistry 69: 2449-2456.
Soltani, B.M., Ehlting, J., Hamberger, B. &
Douglas, C.J. 2006. Multiple Cis-regulatory elements regulate distinct
and complex patterns of developmental and wound-induced expression of Arabidopsis
thaliana 4CL gene family members. Planta 224: 1226-1238.
Souza, A.C., Barbazuk, B., Ralph, S.G.,
Bohlmann, J., Hamberger, B. & Douglas, C.J. 2008. Genome-wide analysis of a
land plant-specific acyl: CoenzymeA synthetase (ACS) gene family in
arabidopsis, poplar, rice and physcomitrella. New Phytologist 179:
987-1003.
Sun, H., Li, Y., Feng, S., Zou, W., Guo, K.,
Fan, C., Si, S. & Peng, L. 2013. Analysis of five rice 4-coumarate:
Coenzyme a ligase enzyme activity and stress response for potential roles in
lignin and flavonoid biosynthesis in rice. Biochemical and Biophysical
Research Communications 430: 1151-1156.
Sykes, R.W., Gjersing, E.L., Foutz, K.,
Rottmann, W.H., Kuhn, S.A., Foster, C.E., Ziebell, A., Turner, G.B., Decker,
S.R., Hinchee, M.A. & Davis, M.F. 2016. Down-regulation of p-coumaroyl
quinate/shikimate 3′-hydroxylase (c3′h) and cinnamate 4-hydroxylase
(c4h) genes in the lignin biosynthetic pathway of Eucalyptus urophylla × Eucalyptus grandis leads to improved sugar release. Biotechnology for
Biofuels 9: 691-699.
Tamura, K., Peterson, D., Peterson, N., Stecher,
G., Nei, M. & Kumar, S. 2011. MEGA5: Molecular evolutionary
genetics analysis using maximum likelihood, evolutionary distance,
and maximum parsimony methods. Molecular Biology and Evolution
28: 2731-2739. Tian, X., Xie, J., Zhao, Y., Lu, H., Liu, S.,
Qu, L., Li, J., Gai, Y. & Jiang, X. 2013a. Sense-, antisense- and RNAi-4CL1
regulate soluble phenolic acids, cell wall components and growth in transgenic Populus
tomentosa Carr. Plant Physiology and Biochemistry 65: 111-119.
Tian, Q., Wang, X., Li, C., Lu, W., Yang, L.,
Jiang, Y. & Luo, K. 2013b. Functional characterization of the poplar
R2R3-MYB transcription factor PtoMYB216 involved in the regulation of lignin
biosynthesis during wood formation. PLoS ONE doi.
10.1371/journal.pone.0076369.
Trabucco, G.M., Matos, D.A., Lee, S.J., Saathoff,
A.J., Priest, H.D., Mockler, T.C., Sarath, G. & Hazen, S.P.
2013. Functional characterization of cinnamyl alcohol dehydrogenase
and caffeic acid o-methyltransferase in Brachypodium distachyon.
BMC Biotechnology doi. 10.1186/1472-6750-13-61. Van Acker, R., Leplé, J.C., Aerts, D., Storme,
V., Goeminne, G., Ivens, B., Légée, F., Lapierre, C., Piens, K., Van Montagu,
M.C. & Santoro, N. 2014. Improved saccharification and ethanol yield from
field-grown transgenic poplar deficient in cinnamoyl-coa reductase. Proceedings
of the National Academy of Sciences of the United States of America 111:
845-850.
Vanholme, R., Demedts, B., Morreel, K., Ralph,
J. & Boerjan, W. 2010. Lignin biosynthesis and structure. Plant
Physiology 153: 895-905.
Voelker, S.L., Lachenbruch, B., Meinzer, F.C.,
Jourdes, M., Ki, C., Patten, A.M., Davin, L.B., Lewis, N.G., Tuskan,
G.A., Gunter, L. & Decker, S.R. 2010. Antisense down-regulation
of 4CL expression alters lignification, tree growth, and saccharification
potential of field-grown poplar. Plant Physiology 154: 874-886.
Wagner, A., Donaldson, L., Kim, H., Phillips, L., Flint, H., Steward, D., Torr, K., Koch, G., Schmitt, U. & Ralph, J. 2009. Suppression of 4-Coumarate-CoA ligase in the coniferous gymnosperm Pinus radiata. Plant Physiology 149: 370-383 Wang, S., Li, E., Porth, I., Chen, J.G., Mansfield,
S.D. & Douglas, C.J. 2014. Regulation of secondary cell wall
biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in
Arabidopsis. Scientific Reports 4: 5054. Wang, T., Zhang, N. & Du, L. 2005. Isolation
of RNA of high quality and yield from Ginkgo biloba leaves.
Biotechnology Letters 27: 629-633. Xu, L., Zhu, L., Tu, L., Liu, L., Yuan, D., Jin,
L., Long, L. & Zhang, X. 2011. Lignin metabolism has a central role in the
resistance of cotton to the wilt fungus Verticillium dahliae as revealed
by RNA-seq-dependent transcriptional analysis and histochemistry. Journal of
Experimental Botany 62: 5607-5621.
Xu, Q., Yin, X.R., Zeng, J.K., Ge, H., Song, M.,
Xu, C.J., Li, X., Ferguson, I.B. & Chen, K.S. 2014. Activator-and
repressor-type MYB transcription factors are involved in chilling injury
induced flesh lignification in loquat via their interactions with the phenylpropanoid
pathway. Journal of Experimental Botany 65: 4349-4359.
Yan, L., Xu, C., Kang, Y., Gu, T., Wang, D.,
Zhao, S. & Xia, G. 2013. The heterologous expression in Arabidopsis
thaliana of sorghum transcription factor SbbHLH1 downregulates lignin synthesis. Journal of Experimental Botany 64: 3021-3032.
Zhang, Z.L., Xie, Z., Zou, X., Casaretto, J.,
Ho, T.H.D. & Shen, Q.J. 2004. A rice WRKY gene encodes a transcriptional
repressor of the gibberellin signaling pathway in aleurone cells. Plant
Physiology 134: 1500-1513.
Zhong, R. & Ye, Z.H. 2009. Transcriptional
regulation of lignin biosynthesis. Plant Signaling & Behavior 4:
1028-1034.
*Corresponding author; email: puad@upm.edu.my |
|||
|
